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The crystal structure of the large ribosomal subunit of Staphylococcus aureus in complex with lefamulin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WCE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 1:2 MPD:EtOH
10mM Hepes pH=7.6
10mM Mg2Cl
60mM NH4Cl
15mM KCl
Crystal Properties Matthews coefficient Solvent content 3.76 67.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 282.112 α = 90 b = 282.112 β = 90 c = 875.343 γ = 120
Symmetry Space Group P 65 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2014-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.971 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 3.55 50 95.7 0.209 0.213 0.055 5 11 236087 105.61
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.55 3.61 94.6 0.994 0.3 0.626 9.2 11504
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4WCE 3.55 49.93 1.35 235811 11845 95.42 0.1888 0.1869 0.1891 0.2266 0.2272 110.8392
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.119 f_angle_d 1.61 f_chiral_restr 0.071 f_bond_d 0.01 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20308 Nucleic Acid Atoms 60413 Solvent Atoms Heterogen Atoms 741
Software Software Software Name Purpose HKL-2000 data collection SCALEPACK data scaling PHENIX refinement PDB_EXTRACT data extraction